Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

De novo construction of isoforms from long-read data

De novo clustering of long transcript reads into genes

Get the consensus sequences from SAM (and BAM) files, ignoring the reference

The source code and results for different methods on annotating external testing datsets of human and mouse.

Alignment-free phylogenomic splits

MUSTANG: reference-free MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance

HUMID: reference free FastQ deduplication

Reference-free FASTQ filter for rare germline and somatic variants

ESKRIM is a reference-free tool that compares microbial richness in shotgun metagenomic samples by counting k-mers

Example of an estimation of cell-type proportions using reference-free method (RefFreeEWAS)

Subtypist is a computational toolkit for subtype identification of single-cell transcriptomic data without reference.

A Nextflow pipeline to generate a phylogenetic tree from SKA alignment